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| − | __NOTOC__
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| − | == Usage ==
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| − | <mmtsbToolUsage cmd="contact.pl"></mmtsbToolUsage>
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| − | == Description ==
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| − | This script calculates residue contact maps and compares them between
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| − | different structures. Residues are considered in contact when the minimum
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| − | inter-residue distance of all pairs of heavy atoms is less than
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| − | 4.2A.<BR>
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| − | In the default mode with two structures as arguments the fraction of contacts
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| − | present in the second structure with respect to the first is determined.
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| − | Also calculated is the continuous quantity rho that uses a sigmoidal function
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| − | for the minimum inter-residue distance around 4.2 A to effectively include
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| − | residue pairs that are slightly further apart with a reduced weight.
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| − | An extended output is available with <B>-list</B> to get a list of all residue
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| − | contacts in the reference structure with the minimum distances in the reference
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| − | as well as the test structures.
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| − | <BR>
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| − | If only one structure is given as an argument no comparison is done. A residue
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| − | contact list is printed out instead. This list can be used in later comparisons
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| − | with <B>-read</B> to save time if multiple structures are compared to the same
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| − | reference. The more costly calculation of the reference residue map then
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| − | has to be done only once.
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| − | <BR>
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| − | The option <B>-l</B> is available to limit the residue map to contacts with
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| − | a subset of residues as might be useful for loop modeling.
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| − | == Options ==
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| − | ; -help : usage information
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| − | == Examples ==
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| − | <mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test1"></mmtsbToolExample>
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| − | <mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test2"></mmtsbToolExample>
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| − | <mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test3"></mmtsbToolExample>
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| − | <mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test4"></mmtsbToolExample>
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